Objective To evaluate the genetic differentiation between Hippophae rhamnoides subsp. sinensis and H. rhamnoides subsp. yunnanensis, to clarify their geographic boundary in ambiguous areas, and estimate the genetic diversity within each taxon.

Method 18 Simple Sequence Repeat (SSR) makers were used to analyze the genetic variation of 32 H. rhamnoides subsp. sinensis and H. rhamnoides subsp. yunnanensis populations. Phylogenetic analysis and cluster analysis were conducted to identify the grouping of these populations according to their morphology and geographic distribution. The genetic differentiation coefficients were calculated among populations within each taxon, and the Analysis of Molecular Variance (AMOVA) was conducted to estimate the variance components at different levels. The genetic diversity parameters, such as allele number (N_A), effective allele number (N_E), observed heterozygosity (H_O), expected heterozygosity (H_E) and inbreeding coefficient (F_IS), were calculated for each taxon and each population.

Result The genetic diversity of H. rhamnoides subsp. sinensis was higher than that of H. rhamnoides subsp. yunnanensis. Compared with H. rhamnoides subsp. yunnanensis, H. rhamnoides subsp. sinensis had lower genetic differentiation coefficients between populations; and AMOVA analysis found that the percentage of variance among populations within taxa was lower in H. rhamnoides subsp. sinensis (25.5%) than in H. rhamnoides subsp. yunnanensis (36.7%), suggesting that the differentiation among geographical populations of H. rhamnoides subsp. sinensis was lower than that of H. rhamnoides subsp. yunnanensis, and the genetic variation of H. rhamnoides subsp. sinensis was mainly between individuals. Phylogenetic analysis suggested that all individuals of H. rhamnoides subsp. sinensis mainly clustered into one clade, while several highly differed clades were found in H. rhamnoides subsp. yunnanensis, and the subsp. sinensis was closer with Sichan subsp. yunnanensis clade than with others. By population genetic cluster analysis, all H. rhamnoides subsp. sinensis and H. rhamnoides subsp. yunnanensis individuals were divided into two major branches, and hybridization between them were found in several populations, especially in populations Hongyuan and Songpan that located in northern Sichuan province.

Conclusion H. rhamnoides subsp. sinensis has higher genetic diversity and lower genetic differentiation than that of H. rhamnoides subsp. yunnanensis. Hongyuan and Songpan counties in northern Sichuan province are most likely to be the distribution boundary between H. rhamnoides subsp. sinensis and H. rhamnoides subsp. yunnanensis.